metadynamics reaction coordinate

From: Rabeta Yeasmin (
Date: Wed Jan 03 2018 - 11:42:57 CST

Dear NAMD Users,

I am trying to run well-tempered metadynamics to find out binding site
between two proteins. I have found some binding sites from docking. I have
used the distance between the mass centres of the two group of atoms in
those two proteins binding sites as reaction coordinate. But after about
running around 10ns, the movement of one protein relative to the other
protein is negligible. I am wondering what kind of reaction coordinate will
be better to move one of the protein through all the possible area of the
other protein.


Rabeta Yeasmin

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